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Density functional slab calculations for adsorption of atoms and molecules on surfaces: Ag/Si(111) and H2/Cu(100) 表面原子和分子吸附的密度泛函板计算:Ag/Si(111)和H2/Cu(100)
Journal of molecular graphics Pub Date : 1996-12-01 DOI: 10.1016/S0263-7855(97)89619-1
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引用次数: 0
Zeneca adopts tripos software Zeneca采用tripos软件
Journal of molecular graphics Pub Date : 1996-12-01 DOI: 10.1016/S0263-7855(96)90035-1
{"title":"Zeneca adopts tripos software","authors":"","doi":"10.1016/S0263-7855(96)90035-1","DOIUrl":"https://doi.org/10.1016/S0263-7855(96)90035-1","url":null,"abstract":"","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 6","pages":"Page 383"},"PeriodicalIF":0.0,"publicationDate":"1996-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(96)90035-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89989175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
New funding for Cherwell Scientific 查威尔科学公司获得新资金
Journal of molecular graphics Pub Date : 1996-12-01 DOI: 10.1016/S0263-7855(96)90038-7
{"title":"New funding for Cherwell Scientific","authors":"","doi":"10.1016/S0263-7855(96)90038-7","DOIUrl":"https://doi.org/10.1016/S0263-7855(96)90038-7","url":null,"abstract":"","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 6","pages":"Page 384"},"PeriodicalIF":0.0,"publicationDate":"1996-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(96)90038-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91592044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Knowledge-based modeling of a legume lectin and docking of the carbohydrate ligand: The Ulex europaeus lectin I and its interaction with fucose 豆科植物凝集素的知识建模和碳水化合物配体的对接:欧叶芥凝集素I及其与焦点的相互作用
Journal of molecular graphics Pub Date : 1996-12-01 DOI: 10.1016/S0263-7855(97)00010-6
Arnaud Gohier , Juan Felix Espinosa , Jesus Jimenez-Barbero , Pierre-Alain Carrupt , Serge Pérez , Anne Imberty
{"title":"Knowledge-based modeling of a legume lectin and docking of the carbohydrate ligand: The Ulex europaeus lectin I and its interaction with fucose","authors":"Arnaud Gohier ,&nbsp;Juan Felix Espinosa ,&nbsp;Jesus Jimenez-Barbero ,&nbsp;Pierre-Alain Carrupt ,&nbsp;Serge Pérez ,&nbsp;Anne Imberty","doi":"10.1016/S0263-7855(97)00010-6","DOIUrl":"10.1016/S0263-7855(97)00010-6","url":null,"abstract":"<div><p>Ulex europaeus isolectin I is specific for fucose-containing oligosaccharide such as H type 2 trisaccharide α-<span>l</span>-Fuc (1→2) β-<span>d</span>-Gal (1→4) β-<span>d</span>-GlcNAc. Several legume lectins have been crystallized and modeled, but no structural data are available concerning such fucose-binding lectin. The three-dimensional structure of <em>Ulex europaeus</em> isolectin I has been constructed using seven legume lectins for which high-resolution crystal structures were available. Some conserved water molecules, as well as the structural cations, were taken into account for building the model. In the predicted binding site, the most probable locations of the secondary hydroxyl groups were determined using the GRID method. Several possible orientations could be determined for a fucose residue. All of the four possible conformations compatible with energy calculations display several hydrogen bonds with Asp-87 and Ser-132 and a stacking interaction with Tyr-220 and Phe-136. In two orientations, the O-3 and O-4 hydroxyl groups of fucose are the most buried ones, whereas two other, the O-2 and O-3 hydroxyl groups are at the bottom of the site. Possible docking modes are also studied by analysis of the hydrophobic and hydrophilic surfaces for both the ligand and the protein. The SCORE method allows for a quantitative evaluation of the complementarity of these surfaces, on the basis of molecular lipophilicity calculations. The predictions presented here are compared with known biochemical data.</p></div>","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 6","pages":"Pages 322-327"},"PeriodicalIF":0.0,"publicationDate":"1996-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(97)00010-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20141671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 18
Simulating the adsorption in porous media: From zeolites to well-bores 模拟多孔介质中的吸附:从沸石到井筒
Journal of molecular graphics Pub Date : 1996-12-01 DOI: 10.1016/S0263-7855(97)89624-5
{"title":"Simulating the adsorption in porous media: From zeolites to well-bores","authors":"","doi":"10.1016/S0263-7855(97)89624-5","DOIUrl":"https://doi.org/10.1016/S0263-7855(97)89624-5","url":null,"abstract":"","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 6","pages":"Page 379"},"PeriodicalIF":0.0,"publicationDate":"1996-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(97)89624-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90017309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular dynamics simulations of polymer melts: The effect of structure generation on gas solubilities 聚合物熔体的分子动力学模拟:结构生成对气体溶解度的影响
Journal of molecular graphics Pub Date : 1996-12-01 DOI: 10.1016/S0263-7855(97)89627-0
{"title":"Molecular dynamics simulations of polymer melts: The effect of structure generation on gas solubilities","authors":"","doi":"10.1016/S0263-7855(97)89627-0","DOIUrl":"10.1016/S0263-7855(97)89627-0","url":null,"abstract":"","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 6","pages":"Page 380"},"PeriodicalIF":0.0,"publicationDate":"1996-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(97)89627-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"97499254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Author/title index 作者/标题索引
Journal of molecular graphics Pub Date : 1996-12-01 DOI: 10.1016/S0263-7855(97)00004-0
{"title":"Author/title index","authors":"","doi":"10.1016/S0263-7855(97)00004-0","DOIUrl":"https://doi.org/10.1016/S0263-7855(97)00004-0","url":null,"abstract":"","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 6","pages":"Pages 391-393"},"PeriodicalIF":0.0,"publicationDate":"1996-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(97)00004-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91634169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
ChemWindow Suite available ChemWindow套件可用
Journal of molecular graphics Pub Date : 1996-12-01 DOI: 10.1016/S0263-7855(96)90047-8
{"title":"ChemWindow Suite available","authors":"","doi":"10.1016/S0263-7855(96)90047-8","DOIUrl":"https://doi.org/10.1016/S0263-7855(96)90047-8","url":null,"abstract":"","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 6","pages":"Page 386"},"PeriodicalIF":0.0,"publicationDate":"1996-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(96)90047-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"137404941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
New version of Accord released 新版本雅阁发布
Journal of molecular graphics Pub Date : 1996-12-01 DOI: 10.1016/S0263-7855(96)90048-X
{"title":"New version of Accord released","authors":"","doi":"10.1016/S0263-7855(96)90048-X","DOIUrl":"https://doi.org/10.1016/S0263-7855(96)90048-X","url":null,"abstract":"","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 6","pages":"Page 386"},"PeriodicalIF":0.0,"publicationDate":"1996-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(96)90048-X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"137404942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
HOLE: A program for the analysis of the pore dimensions of ion channel structural models HOLE:用于分析离子通道结构模型孔隙尺寸的程序
Journal of molecular graphics Pub Date : 1996-12-01 DOI: 10.1016/S0263-7855(97)00009-X
Oliver S. Smart , Joseph G. Neduvelil , Xiaonan Wang , B.A. Wallace , Mark S.P. Sansom
{"title":"HOLE: A program for the analysis of the pore dimensions of ion channel structural models","authors":"Oliver S. Smart ,&nbsp;Joseph G. Neduvelil ,&nbsp;Xiaonan Wang ,&nbsp;B.A. Wallace ,&nbsp;Mark S.P. Sansom","doi":"10.1016/S0263-7855(97)00009-X","DOIUrl":"10.1016/S0263-7855(97)00009-X","url":null,"abstract":"<div><p>A method (HOLE) that allows the analysis of the dimensions of the pore running through a structural model of an ion channel is presented. The algorithm uses a Monte Carlo simulated annealing procedure to find the best route for a sphere with variable radius to squeeze through the channel. Results can be displayed in a graphical fashion or visualized with most common molecular graphics packages. Advances include a method to analyze the anisotropy within a pore. The method can also be used to predict the conductance of channels using a simple empirically corrected ohmic model. As an example the program is applied to the cholera toxin B-subunit pentamer. The compatibility of the crystal structure and conductance data is established.</p></div>","PeriodicalId":73837,"journal":{"name":"Journal of molecular graphics","volume":"14 6","pages":"Pages 354-360"},"PeriodicalIF":0.0,"publicationDate":"1996-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/S0263-7855(97)00009-X","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"20141010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1299
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